Two schools (each composed of fifty students, hence the name of the show) competed in a variety of contests, with points awarded for success, and the school with the most points was the winner. In the first series, the teams were coloured orange and green. From the second series onward, they were blue and yellow.

Each member of each team wore a pin, each with a different number from 1 to 50. Flynn would randomly select some of the numbers and those contestants (from either team) would play a game. The games could be either physical or quiz rounds. Each number was used only once per show. Not all the contestants played a game, but they did all take part in an observation round where points were earned based on how many of them answered the same question correctly.

Each episode featured a variety of contests. In earlier series, these were larger forms of simple activities. Until the fifth series, some of the physical games had a quiz at the end of an obstacle course. These were soon removed from the show, and general knowledge was only tested in the quizzes.

The Rollometer – This was typically the first game of the show between the fifth and seventh series. In this game contestants would jump onto a giant, rocky, inflatable round table with a giant sphere hanging above them. Contestants had to jump up and collect either a blue or yellow tag depending on their team colour whilst also trying to keep their balance on the table. There were also a few gold tags which were situated a little higher than the team colours. 10 points were awarded if the players got a tag of their team colour and 20 points were given for a golden tag. In the last two series, the tags were star-shaped and the gold tags were replaced by red 'mystery stars'. They could increase a score or score 0 (or, in the last series, even decrease a score). The score was displayed inside the mystery star.

The Spike – This was only used in the eighth and ninth series, and it was typically the first game of the show. Four contestants had to battle their way through a forest of spikes, then through a 'spiky jaw'. After climbing up a hill, they had to collect one puzzle piece hanging above the top of the hill, slide down the other side of the hill and hand the puzzle piece over to their team's selected 'builder', who sloted the puzzle of four pieces of the number 50 into the correct space. Each puzzle piece was worth 10 points, and the first team to complete the puzzle scored a 30-point bonus, making a total of 70 points.

The Observator – The two teams were shown part of a music video. They were then asked five questions relating to specific details in the video. Each team member answered either true or false on a keypad. If any of them got it right, they each scored one point for their team. When Angelica Bell was the host, it was played before The Avalanche. When Sophie McDonnell was the host, it was played after the first time one team played The Cube or The Wire. This contest was also used as a tiebreaker round in the event that a tie occured at the end of the game.

The Pulse – This was known as "The Brainbuster" until the last episode of Series 8. A player was picked at random to answer a general knowledge question. They can play – get it right and score 100 points, get it wrong and they score nothing – or pass – their team-mates will vote on the question in the same manner as The Observator, with a maximum of 50 points.

50 to 1 - This was only played when Sally Gray was the host in the fifth and sixth series. This was played in a similar way to "The Pulse". Questions were fired at alternate teams. A number was randomly selected in a faster-paced manner than in "The Pulse". The question was then immediately asked with no optional choices. The contestant had three seconds to answer. They could answer alone for 20 points or pass the question over to their team-mates by saying, "50 to 1". Three optional choices were displayed and the team members voted on their keypads. The chosen contestant then selected one of the three answers with the help of the voting results (displayed in percentages on Flynn's screen). They could go against the team's most popular answer if they wanted; however, only five points is scored for a right answer in this situation. A wrong answer or no answer within three seconds scores 0.

The Revolve – One-by-one, contestants had to pass an obstacle course and enter a revolving maze. There were puzzle pieces hanging above the centre. This worked in much the same way as The Spike – four randomly picked contestants would get to the centre of the maze, grab a puzzle piece in their team's colour, get out of the maze and hand the piece to their builder who would build the puzzle. 20 points were scored for each piece on the table. Completing the puzzle first was worth a 40-point bonuss, making a total of 120 points.

The Cube – A team captain would insert a ball inside a large, tiltable Perspex cube. Four contestants would guide the ball by tilting each corner of the cube. At various points within three layers were holes to drop the ball into, and at the bottom was a Hit Zone (20 points for the first two, 40 points for any others) and a Miss Zone (lose 10 points). There was also a chute that would give the team a direct Hit. The game music is the same music for The Tensioner.

The Square – This had the same rules as The Cube, but teams were restricted to only using 2 dimensions at a time. This was played before the introduction of The Cube, which replaced this game.

The Wire – This was only played when Sophie McDonnell was the host in the final series. Each player in a team of five had to manoeuvre a hoop along a wired section. Each completed section scored 20 points. 5 points were deducted any time the hoop touched the wire. After each section, the hoops would reduce in diameter. An extra 20 points was scored if the whole course was completed within 2 minutes. If the time limit expired, the game would end. Each player also had to maintain their balance on a section of very small hills and horizontal hoops along the way.

The Elevator – Players would release a series of balls into a chute, which would be fired from the end of a funnel held by the team's 'shooter'. They then had to race the balls by climbing up and sliding down an inflatable hill (previously a 'bish-bash' and then a mangle) to get to their team's shooter. By moving the end of a pivoted, long-tailed seat downwards to raise the shooter high in the air, the shooter aimed at a chute as the balls are released. The balls had fill the tube to the designated score marker (the lowest being 20, then 40, 60, 80 and 120) to achieve the points. In the later series, each ball scored 10 points but the score markers remained (this time in increments of 30) and a lid was installed above the chute, which opens when the shooter is elevated, to prevent the shooter attempting to score from ground level.

The Fly – Each player would grab a suction cup, race along an obstacle course whilst holding it, and hand it to their team's 'fly' – a player hooked up to the roof. By placing the suction cups on a table, the fly would pull himself/herself along. The last suction cup would be used to open a pyramid. Inside the pyramid was a plunger which the fly would then hit. Each suction cup was worth 10 points if correctly placed, and the first to the plunger would get an 30-point bonus. In the later series, crossed-over wires were installed a few inches above the surface. Should the fly touch the wire, they had to return to the back and try again.

The Tensioner – This was only played when Sally Gray was the host. The team that had the least points after The Pulse would play this game. This was the only game to have two players from one team. The two players were attached to The Tensioner with horizontal bungee ropes and they had to work together to avoid setting off the alarm as they made their way over the obstacles and up the course. If the ball touched either of the metal horizontal tubes, the alarm would sound and the two players had to return to the previous footsteps and start again. If a player stood on the footprints, they scored 20/40 points. The team had to walk backwards. This did not appear in the late series due to an appearance of The Cube and then The Wire, although its game music was kept for the former.

The Bridge – This was only played when Sally Gray was the host. Each team was be given a metal bridge to use between some islands in a group and they had to make sure they pickd up these crystals. When they got to the end, they had to place the crystals in the correct holes. Their feet couldn't touch the ground; otherwise, the team had to return to the start.

The Stinger – This was only played when Sally Gray and Angellica Bell hosted the show. The players had to guide "The Stinger" - a long metal rod attached by four ropes - through the course to pass it from one zone to the next. Each zone was worth 10 points and there were eight in total. One player acted as the captain and gave advice to the other four players guiding The Stinger by pulling and moving the ropes. If the stinger touched the edges before reaching the next zone, the team had to return The Stinger to the previous zone and start again from there.

The Avalanche – Consisting teams of six (originally eight), each player had to battle through a small tunnel. In front of them were spiked stalagmites jutting out of the surface of the inflatable with snowflakes stuck on them (in the earlier series, there were white snowflakes, placed evenly, but in the later episodes there was a white snowflake above a gold one on each stalagmite). They then had to move past a pair of giant snowballs and a pair of giant ice cubes, climb up a hill on an attached cargo net, slide down the other side and press their team's snowdome to secure their points. Each player that hit the snowdome scored 30 points, white snowflakes were worth 50 points and gold snowflakes were worth 80 points. They could head for the snowdome without a snowflake to save time, but only one snowflake per player could be taken. If a player didn't press a snowdome before the end of the game, neither the snowflake nor the snowdome would count. The Avalanche was usually the last game of each episode.